Refereed Journal Articles

Appuhamy, J. A. D. R. N, B. G. Cassell, and J. B. Cole. 2009. Phenotypic and genetic relationships between common health disorders and milk and fat yield persistencies from producer recorded health data and test day yields. Journal of Dairy Science 92:1785-1795

Appuhamy, J. A. D. R.N., B. G. Cassell, C. D. Dechow, and J. B. Cole. 2007. Phenotypic relationships of common health disorders in dairy cows to lactation persistency estimated from daily milk weights. Journal of Dairy Science 90:4424-4434.

Attalla, S. A., A. J. Seykora, J. B. Cole, and B. J. Heins. 2010. Genetic parameters of milk ELISA scores for Johne's disease. Journal of Dairy Science 93:1729-1735.

Bohmanova, J., I. Misztal, and J. B. Cole. 2007. Comparison of seven temperature humidity indices as indicators of milk production losses due to heat stress in semi-arid and humid climates. Journal of Dairy Science 90:1947-1956.

Cole, J. B. 2007. PyPedal: A package for pedigree analysis using the Python programming language. Computers and Electronics in Agriculture 57:107-113.

Cole, J. B., D. E. Franke, and E. A. Leighton. 2004. Population genetic structure of a colony of German Shepherd and Labrador Retriever dog guides. Journal of Animal Science 82:2906-2912.

Cole, J. B., R. C. Goodling, Jr., G. R. Wiggans, and P. M. VanRaden. 2005. Genetic evaluation of calving ease for Brown Swiss and Jersey bulls from purebred and crossbred calvings. Journal of Dairy Science 88:1529-1539.

Cole, J. B., and D. J. Null. 2009. Genetic evaluation of lactation persistency for five breeds of dairy cattle. Journal of Dairy Science 92:2248-2258.

Cole, J. B., D. J. Null, A. H. Sanders, and J. S. Clay. 2008. Use of producer-recorded health event data in genetic evaluation. I. Validation of data from on-farm computer systems. Journal of Dairy Science (in preparation)

Cole, J. B., T. S. Sonstegard, L. Ma, G. R. Wiggans, B. A. Crooker, C. P. Van Tassell, J. Yang, L. K. Matukumalli, and Y. Da. 2010. Refinted QTL detection through genome-wide association analysis of contemporary U.S. Hosltein cows: I. Production, health, and reproduction. Physiological Genomics (submitted)

Cole, J. B.,, and P. M. VanRaden. 2010. Visualization of results from genomic evaluations. Journal of Dairy Science 93:2727-2740.

Cole, J. B., D. J. Null, and P. M. VanRaden. 2009. Best prediction of yields for long lactations. Journal of Dairy Science 92:1796-1810.

Cole, J. B., P. M. VanRaden, J. R. O'Connell, C. P. Van Tassell, T. S. Sonstegard, R. D. Schnabel, J. F. Taylor, and G. R. Wiggans. 2009. Distribution and location of genetic effects for dairy traits. Journal of Dairy Science 92:2931-2946.

Cole, J. B., and P. M. VanRaden. 2006. Genetic evaluation and best prediction of lactation persistency. Journal of Dairy Science 89:2722-2728.

Cole, J. B., G. R. Wiggans, and P. M. VanRaden. 2007. Genetic evaluation of stillbirth in United States Holsteins using a sire-maternal grandsire threshold model. Journal of Dairy Science 90:2480-2488.

Cole, J. B., G. R. Wiggans, P. M. VanRaden, and R. H. Miller. 2007. Stillbirth (co)variance components for a sire-maternal grandsire threshold model and development of a calving ability index for sire selection. Journal of Dairy Science 90:2489-2496.

Hansen, L. B., J. B. Cole, G. D. Marx, and A. J. Seykora. 1999. Productive life and reasons for disposal of Holstein cows selected for large versus small body size. Journal of Dairy Science 82:795-801.

Miller, R. H., H. D. Norman, J. R. Wright, and J. B. Cole. 2008. Relationship of productive life of daughters to predicted transmitting ability milk somatic cell score of their sires and maternal grandsires. Journal of Dairy Science 92:2224-2228.

Norman, H. D., J. R. Wright, M. T. Kuhn, S. M. Hubbard, J. B. Cole, and P. M. VanRaden. 2009. Genetic and environmental factors that impact gestation length. Journal of Dairy Science 92:2259-2269.

Rohli, R. V., M. M. Russo, A. J. Vega, and J. B. Cole. 2004. Atmospheric and statewide anomalously-high tropospheric ozone concentrations in Louisiana. Journal of Applied Meteorology 43:1438-1451.

Sonstegard, T. S., L. Ma, J. B. Cole, G. R. Wiggans, C. P. Van Tassell, G. Liu, B. D. Mariani, B. A. Crooker, P. M. VanRaden, M. V. da Silva, and Y. Da. 2008. Genomic signatures of artificial selection in U.S. Holstein cows. Nature Genetics (in preparation)

VanRaden, P. M., M. E. Tooker, J. B. Cole, G. R. Wiggans, and J. H. Megonigal, Jr. 2007. Genetic evaluations for mixed breed populations. Journal of Dairy Science 90:2434-2441.

Wiggans, G. R., J. B. Cole, and L. L. M.Thornton. 2008. Multiparity evaluation of calving ease and stillbirth with separate genetic effects by parity. Journal of Dairy Science 91:3173-3178.

Book Chapters and Technical Reports

Cole, J. B. 2007. AIPL Research Report SB1: Genetic evaluation of stillbirth. Available: http://aipl.arsusda.gov/reference/fertility/sb2006.html.

Cole, J. B. 2005. AIPL Research Report CE1: Brown Swiss and Holstein calving ease. Available: http://aipl.arsusda.gov/reference/fertility/ce2005.htm.

de Vries, A., and J. B. Cole. 2008. Profitable dairy cow traits for hot climatic conditions in Breeding for robustness in cattle -- EAAP 126 (M. Klopcic, R. Reents, J. Philipsson, and A. Kuipers, Eds.) Wageningen Academic Publishers, Waginengen, The Netherlands.

Lanting, F. L., and J. B. Cole. 2004. Chapter 13: Basics of Genetics. Pages 256-290 in The Total German Shepherd Dog, 2nd ed. Hoflin Publishing, Wheat Ridge, CO.

Popular Press Articles

Cole, J. B. 2008. Using Python to study pedigrees with PyPedal. Python Magazine (accepted)

Cole, J. B. 2005. How can we genetically improve dairy cattle health? The Dairy Focus 6(4):3.

Cole, J. B., R. C. Goodling, Jr., G. R. Wiggans, and P. M. VanRaden. 2006. Genetic calving ease study on crossbreeds. Jersey Journal 53(5):83-84.

Seykora, A. J., P. M. VanRaden, and J. B. Cole. 2006. Net Merit receives face-lift. Hoard's Dairyman 151(14):557.

Proceedings

Appuhamy, J. A. D. R. N., B. G. Cassell, and J. B. Cole. 2006. Effect of mastitis and postpartum metabolic diseases on lactation persistency of Holstein and Jersey cows. Journal of Dairy Science 89(Suppl. 1):398(abstr. 476).

Cole, J. B. 2008. Data collection ratings and best prediction of lactation yields. International Committee on Animal Recording Proceedings. ICAR Technical Series. 13:403-406.

Cole, J. B., and D. E. Franke. 2002. PyPedal: A package for pedigree analysis using the Python programming language. Journal of Animal Science 80 (Suppl. 1):323(abstr. 1291)

Cole, J. B., D. E. Franke, and E. A. Leighton. 2003. Genetic parameters for longevity in a colony of German Shepherd dog guides. Journal of Animal Science 81 (Suppl. 1):197(abstr. M76)

Cole, J. B., D. E. Franke, and E. A. Leighton. 2003. Population genetic structure of a colony of German Shepherd and Labrador Retriever dog guides. Journal of Animal Science 81 (Suppl. 1):69(abstr. 272)

Cole, J. B., L. B. Hansen, and G. D. Marx. 1997. Productive life, reasons for disposal, and body dimensions and weights of Holsteins selected for large versus small body size. Journal of Dairy Science 80(Suppl. 1): 252(abstr. P423)

Cole, J. B., and E. A. Leighton. 2004. Linear versus threshold model analysis of trainability in a colony of German Shepherd dog guides. Journal of Animal Science 87(Suppl. 1):391(abstr. 648)

Cole, J. B., H. D. Norman, and P. D. Miller. 2004. Genetic improvement of dairy cattle health in Proceedings of the 12th International Conference on Production Diseases in Farm Animals, July 19-22, 2004, East Lansing, MI. p. 78.

Cole, J. B., and D. J. Null. 2007. Genetic evaluation of lactation persistency estimated by best prediction for Ayrshire, Brown Swiss, Guernsey, and Milking Shorthorn dairy cattle. Journal of Dairy Science 90(Suppl. 1):20(abstr. M52)

Cole, J. B., D. J. Null, and L. R. Bacheller. 2008. A data exchange format and national database for producer-recorded health event data from on-farm management software. Journal of Dairy Science 91(E-Suppl. 1):2-3(abstr. T6)

Cole, J. B., A. H. Sanders, and J. S. Clay. 2006. Use of producer-recorded health data in determining incidence risks and relationships between health events and culling. Journal of Dairy Science 89(Suppl. 1):10(abstr. M7).

Cole, J. B., and A. H. Sanders. 2005. Genetic evaluation of clinical mastitis in U.S. dairy cattle in Lamont, S.J., M. F. Rothschild, and D. L. Harris, editors. Proceedings of the Third International Symposium on Genetics of Animal Health, July 13-15, 2005, Ames, Iowa. p. 112.

Cole, J. B., B. R. Southey, D. E. Franke, and E. A. Leighton. 2007. Discrete time survival analysis of longevity in a colony of dog guides in Proceedings of 5th International Working Dog Breeding Conference, San Antonio, TX.

Cole, J. B., B. R. Southey, D. E. Franke, and E. A. Leighton. 2005. Discrete time survival analysis of longevity in a colony of dog guides. Journal of Animal Science 83 (Suppl. 1):103(abstr. 136).

Cole, J. B., M. E. Tooker, P. M. VanRaden, and J. H. Megonigal. 2004. Breed composition codes for crossbred dairy cattle in the United States. Journal of Dairy Science 87(Suppl. 1):284(abstr. 536).

Cole, J.B. and P. M. VanRaden. 2010. Use of haplotypes to estimate Mendelian sampling effects and selection limits. Proceedings of the 9th World Congress on Genetics Applied to Livestock Production, Aug. 1-6, 2010, Leipzig, Germany.

Cole, J. B., and P. M. VanRaden. 2005. Genetic evaluation and best prediction of lactation persistency. Journal of Dairy Science 88 (Suppl. 1):379-380(abstr. 651).

Cole, J. B., P. M. VanRaden, and C. M. B. Dematawewa. 2007. Estimation of yields for long lactations using best prediction. Journal of Dairy Science 90(Suppl. 1):421(abstr. 558).

Cole, J. B., P. M. VanRaden, J. R. O'Connell, C. P. Van Tassell, and R. D. Schnabel. 2008. Distribution and location of genetic effects for dairy traits. International Committee on Animal Recording Proceedings. ICAR Technical Series. 13:355-360.

Cole, J.B., G. R. Wiggans, L. Ma, T. S. Sonstegard, B. A. Crooker, C. P. Van Tassell, J. Yang, L. K. Matukumalli, and Y. Da, Y.. 2010. High resolution QTL maps of 31 traits in contemporary U.S. Holstein cows. Proceedings of the 9th World Congress on Genetics Applied to Livestock Production, Aug. 1-6, 2010, Leipzig, Germany.

Cole, J. B., G. R. Wiggans, and P. M. VanRaden. 2006. Genetic evaluation of stillbirth in United States Holsteins using a sire-maternal grandsire threshold model. Comm. 01-28 in Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Brazil.

Cole, J. B., G. R. Wiggans, P. M. VanRaden, and R. H. Miller. 2006. Stillbirth (co)variance components for a sire-maternal grandsire threshold model. Journal of Dairy Science 89(Suppl. 1):273(abstr. 339).

Hansen, L. B., J. B. Cole, and G. D. Marx. 1998. Body size of lactating dairy cows: Results of divergent selection for over 30 years. Proceedings of the 6th World Congress on Genetics Applied to Livestock Production, Armidale, NSW, Australia XXV:35-38.

Norman, H. D., J. R. Wright, M. T. Kuhn, S. M. Hubbard, and J. B. Cole. 2007. Genetic and environmental factors that affect gestation length. Journal of Dairy Science 90(Suppl. 1):264 (abstr. T73)

Norman, H. D., J. R. Wright, and J. B. Cole. 2007. Effect of temperature and humidity on gestation length. Journal of Dairy Science 90(Suppl. 1):16(abstr. M38)

Norman, H. D., J. R. Wright, P. M. VanRaden, and J. B. Cole. 2007. Effect of service sire and cow sire on gestation length. Journal of Dairy Science 90(Suppl. 1):194(abstr. 230)

Sonstegard, T. S., L. Ma, J. B. Cole, G. R. Wiggans, C. P. Van Tassell, G. Liu, B. D. Mariani, B. A. Crooker, P. M. VanRaden, M. V. da Silva, and Y. Da. 2008. Genomic signatures of artificial selection in U.S. Holstein cows. International Society for Animal Genetics Proceedings (Poster 638 2098)

Sonstegard, T. S., L. Ma, J. B. Cole, G. R. Wiggans, B. A. Crooker, C. P. Van Tassell1, B. D. Mariani, and Y. Da . 2009. Genome signature of artificial selection for high milk yield in Holstein cattle. Plant and Animal Genome XVII Proceedings. (accepted)

VanRaden, P. M., M. E. Tooker, and J. B. Cole. 2004. Heterosis and breed differences for daughter pregnancy rate in crossbred dairy cows. Journal of Dairy Science 87(Suppl. 1):284(abstr. 532)

VanRaden, P. M., M. E. Tooker, J. B. Cole, G. R. Wiggans, and J. H. Megonigal, Jr. 2006. Genetic evaluations for mixed breed populations. Journal of Dairy Science 89(Suppl. 1):98(abstr. 40).

Wiggans, G. R., J. B. Cole, and L. L. M. Thornton. 2007. Multitrait evaluation for calving ease and stillbirth with separate genetic effects by parity. Journal of Dairy Science 90(Suppl. 1):377(abstr. 422).

Wiggans, G. R., C. P. Van Tassell, J. B. Cole, and L. L. M. Thornton. 2006. Genetic correlations between first and later parity calving ease in a sire-maternal grandsire model. Comm. 01-92 in Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Brazil.

Software

Cole, J. B. 2005. PyPedal: A package for pedigree analysis using the Python programming language, v. 2.0.0. Website: http://pypedal.sourceforge.net/.

Cole, J. B., and P. M. VanRaden. 2007. A Manual for Use of BESTPRED: A Program for Estimation of Lactation Yield and Persistency Using Best Prediction. Website: http://www.aipl.arsusda.gov/software/bestpred/.